Data from: A dedicated target capture approach reveals variable genetic markers across micro- and macro-evolutionary time scales in palms

Understanding the genetics of biological diversification across micro- and macro-evolutionary time scales is a vibrant field of research for molecular ecologists as rapid advances in sequencing technologies promise to overcome former limitations. In palms, an emblematic, economically and ecologically important plant family with high diversity in the tropics, studies of diversification at the population and species levels are still hampered by a lack of genomic markers suitable for the genotyping of large numbers of recently diverged taxa. To fill this gap, we used a whole genome sequencing approach to develop target sequencing for molecular markers in 4,184 genome regions, including 4,051 genes and 133 non-genic putatively neutral regions. These markers were chosen to cover a wide range of evolutionary rates allowing future studies at the family, genus, species and population levels. Special emphasis was given to the avoidance of copy number variation during marker selection. In addition, a set of 149 well-known sequence regions previously used as phylogenetic markers by the palm biological research community were included in the target regions, to open the possibility to combine and jointly analyse already available data sets with genomic data to be produced with this new toolkit. The bait set was effective for species belonging to all three palm subfamilies tested (Arecoideae, Ceroxyloideae and Coryphoideae), with high mapping rates, specificity and efficiency. The number of high quality Single Nucleotide Polymorphisms (SNPs) detected at both the subfamily and population levels facilitates efficient analyses of genomic diversity across micro- and macro-evolutionary time scales.解析微观与宏观进化时间尺度下生物多样化的遗传机制，是当前分子生态学家蓬勃发展的研究领域，测序技术的快速进步有望打破此前的研究局限。棕榈科是一类兼具标志性意义、经济与生态价值且在热带地区物种多样性极高的植物类群，然而针对其种群与物种层级多样化的研究，仍因缺乏适用于大量新近分化类群基因分型的基因组标记而受阻。为填补这一研究空白，本研究采用全基因组测序策略，开发了覆盖4184个基因组区域的分子标记靶向测序体系，其中包含4051个基因区域与133个推定呈中性的非基因区域。这些标记的选取覆盖了广泛的进化速率范围，可支持未来在科、属、种乃至种群层级的相关研究。在标记筛选过程中，本研究特别注重规避拷贝数变异（copy number variation）。此外，本研究纳入了棕榈生物研究领域此前常用作系统发育标记的149个经典序列区域，以实现将现有已公开数据集与本新型靶向测序工具产生的基因组数据进行联合整合与协同分析。该捕获探针组对本次测试涉及的全部3个棕榈亚科类群均有效，即槟榔亚科（Arecoideae）、蜡椰亚科（Ceroxyloideae）与扇叶棕榈亚科（Coryphoideae），且具有较高的比对率、特异性与捕获效率。本研究在亚科与种群层级均检测到大量高质量单核苷酸多态性（Single Nucleotide Polymorphisms，SNPs），可有效支撑微观与宏观进化时间尺度下的基因组多样性分析。